[gmx-users] Changing Sigma in force field

Mark Abraham mark.j.abraham at gmail.com
Mon Aug 27 09:34:03 CEST 2018


Does your topology actually refer to the new atom type? If so, you can
prove it by commenting out the definition of the atom type, and see that
grompp complains about it.


On Wed, Aug 22, 2018 at 4:59 PM hosein geraili <geraili_hosein at yahoo.com>

> Dear all,I am trying to change the epsilon of one atom type in the Amber
> force field, and because I have some atom in this type that I don't want to
> be changed, I defined a new atom type. I mean I add in all the files in the
> force field.ff directory that has that atom type a new atom type with a new
> name and new value for Sigma, but all the other thing are the same for this
> new atomtype, and then changed the aminoacids in the aminoacids.rtp file
> that I want to implement this change the atom type to this new one. But it
> doesn't work when I test it with one step MD for one aminoacid and one
> water. I also checked and if I change the value of Sigma for the already
> defined type the test answers properly. What am I missing here???Best
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